Alignments for a candidate for gcvT in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvT in Stenotrophomonas chelatiphaga DSM 21508

Align aminomethyltransferase; EC 2.1.2.10 (characterized)
to candidate WP_057687195.1 ABB28_RS15055 glycine cleavage system protein T

Query= CharProtDB::CH_000563
         (364 letters)



>NCBI__GCF_001431535.1:WP_057687195.1
          Length = 370

 Score =  381 bits (979), Expect = e-110
 Identities = 202/368 (54%), Positives = 249/368 (67%), Gaps = 12/368 (3%)

Query: 1   MAQQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGS 60
           M Q+T L + H   GA+MVDF GW MP+HYGSQ+DEHH VR +AG+FDVSHMT+VDLRG 
Sbjct: 1   MTQKTLLNDSHRALGAKMVDFGGWDMPIHYGSQLDEHHLVRREAGVFDVSHMTVVDLRGE 60

Query: 61  RTREFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREK 120
           + + FLR LLAN V KL  +GKALYS MLN  GGVIDDLIVYY  +DFFR+VVN++TREK
Sbjct: 61  QVKPFLRRLLANSVDKLKVTGKALYSCMLNERGGVIDDLIVYYLADDFFRMVVNASTREK 120

Query: 121 DLSWITQHAEPFGIEITVRDDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQAG 180
           DL+W+T  A PFG+ +  R DL+++AVQGP A+     L + A    +  +  F   +  
Sbjct: 121 DLAWLTAQAAPFGVAVQQRPDLAILAVQGPQARDAVIGLVDAAGAATLAKLARFAATEVT 180

Query: 181 D-----LFIATTGYTGEAGYEIALPNEKAADFWRALVEAGVKPCGLGARDTLRLEAGMNL 235
                 LF+A TGYTGE G+EI LP +    FW  L++AGVKP GLGARDTLRLEAGMNL
Sbjct: 181 SADGVALFVARTGYTGEDGFEILLPQDAVVAFWNQLLQAGVKPAGLGARDTLRLEAGMNL 240

Query: 236 YGQEMDETISPLAANMGWTIAWEPADRDFIGREALEVQREHG-TEKLVGLVMTEKGVLRN 294
           YGQ+MDE I+P  A + WT++ +   RDFIGR+ LE Q+  G   +++GLVM EKGVLR+
Sbjct: 241 YGQDMDEAITPYEAALAWTVSLDEG-RDFIGRDVLEAQKAAGDARQMIGLVMDEKGVLRH 299

Query: 295 ELPVRFTDAQGNQHEGIITSGTFSPTLGYSIALARVPEGIGETAIVQIRNREMPVKVTKP 354
              V     QG      I SGTFSPTL   IA ARVP G      V IR R +PV+V K 
Sbjct: 300 GQAVLTAGGQGE-----ILSGTFSPTLAKGIAFARVPAGELGAVSVDIRGRAVPVRVVKF 354

Query: 355 VFVRNGKA 362
            FVR G+A
Sbjct: 355 PFVREGQA 362


Lambda     K      H
   0.320    0.136    0.402 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 457
Number of extensions: 19
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 364
Length of database: 370
Length adjustment: 30
Effective length of query: 334
Effective length of database: 340
Effective search space:   113560
Effective search space used:   113560
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate WP_057687195.1 ABB28_RS15055 (glycine cleavage system protein T)
to HMM TIGR00528 (gcvT: glycine cleavage system T protein (EC 2.1.2.10))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR00528.hmm
# target sequence database:        /tmp/gapView.21268.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00528  [M=362]
Accession:   TIGR00528
Description: gcvT: glycine cleavage system T protein
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.8e-132  425.9   0.0   6.6e-132  425.7   0.0    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057687195.1  ABB28_RS15055 glycine cleavage s


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057687195.1  ABB28_RS15055 glycine cleavage system protein T
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  425.7   0.0  6.6e-132  6.6e-132       2     361 ..       3     358 ..       2     359 .. 0.97

  Alignments for each domain:
  == domain 1  score: 425.7 bits;  conditional E-value: 6.6e-132
                                 TIGR00528   2 krtpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLqrlla 70 
                                               ++t L d h  lg+k+vdf+Gw +P++y+s+ +eh+ vr +aG+fDvshm+ v+l+G+++  fL+rlla
  lcl|NCBI__GCF_001431535.1:WP_057687195.1   3 QKTLLNDSHRALGAKMVDFGGWDMPIHYGSQLDEHHLVRREAGVFDVSHMTVVDLRGEQVKPFLRRLLA 71 
                                               79******************************************************************* PP

                                 TIGR00528  71 nDvdaLtk.GkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtls 138
                                               n vd+L + Gka+ys +ln  GGv+DDlivy+ ++d +f++vvna+t+ekDl+wl+ ++++++   +++
  lcl|NCBI__GCF_001431535.1:WP_057687195.1  72 NSVDKLKVtGKALYSCMLNERGGVIDDLIVYYLADD-FFRMVVNASTREKDLAWLTAQAAPFGVAVQQR 139
                                               ******999***************************.******************************** PP

                                 TIGR00528 139 keisllalqGPkaktiledlldkaveg.lkefffvqeaelalkka...liartGytGedGfeiavanek 203
                                                ++++la+qGP+a++ +  l+d+a  + l +++   ++e++  ++   ++artGytGedGfei ++++ 
  lcl|NCBI__GCF_001431535.1:WP_057687195.1 140 PDLAILAVQGPQARDAVIGLVDAAGAAtLAKLARFAATEVTSADGvalFVARTGYTGEDGFEILLPQDA 208
                                               ***************99999998765559****999****99999999********************* PP

                                 TIGR00528 204 avelwkklveaygvkPiGLgarDtLrleagmaLyGqeldeeitPleaglgwvvkkerkksdfiGravle 272
                                                v +w++l++a gvkP GLgarDtLrleagm+LyGq++de itP ea+l w+v+++ + +dfiGr+vle
  lcl|NCBI__GCF_001431535.1:WP_057687195.1 209 VVAFWNQLLQA-GVKPAGLGARDTLRLEAGMNLYGQDMDEAITPYEAALAWTVSLD-EGRDFIGRDVLE 275
                                               ***********.********************************************.9*********** PP

                                 TIGR00528 273 eqkengtekklvGlemlekgiarnelkvlltngekevGivtsGtlsPtLgknialayvdkelekiGtkl 341
                                                qk+ g  ++++Gl+m ekg++r++  vl++ g    G + sGt+sPtL k ia a+v+    + G  +
  lcl|NCBI__GCF_001431535.1:WP_057687195.1 276 AQKAAGDARQMIGLVMDEKGVLRHGQAVLTAGG---QGEILSGTFSPTLAKGIAFARVP--AGELG-AV 338
                                               ******************************666...9**********************..45666.68 PP

                                 TIGR00528 342 evevrnklvkikvvkklfvr 361
                                                v++r++ v+++vvk +fvr
  lcl|NCBI__GCF_001431535.1:WP_057687195.1 339 SVDIRGRAVPVRVVKFPFVR 358
                                               9*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (370 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 12.09
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources